Variant report

Variant	rs6998334
Chromosome Location	chr8:19348020-19348021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10088454	0.87[CHD][hapmap]
rs10089231	0.86[CHD][hapmap]
rs10101192	0.87[CHD][hapmap]
rs10105097	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10105363	0.82[CHD][hapmap]
rs10109274	0.87[CHD][hapmap]
rs1013438	0.87[CEU][hapmap]
rs10503653	0.82[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10888165	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11204045	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11204046	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204047	0.92[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204048	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204049	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204050	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11204052	0.86[ASN][1000 genomes]
rs11777566	0.83[ASN][1000 genomes]
rs11778734	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11780475	0.88[ASN][1000 genomes]
rs11783263	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12682196	0.89[JPT][hapmap]
rs13250181	0.89[JPT][hapmap]
rs13261442	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13261732	0.89[JPT][hapmap]
rs13265751	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13266857	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13267265	0.93[ASN][1000 genomes]
rs13267569	0.93[ASN][1000 genomes]
rs13276417	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13280711	0.88[ASN][1000 genomes]
rs13282951	0.87[CHD][hapmap]
rs17128525	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17128556	0.87[CHD][hapmap]
rs17128604	0.82[CHD][hapmap]
rs17479777	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28490401	0.87[CHD][hapmap]
rs28671342	0.89[ASN][1000 genomes]
rs2958576	0.87[CEU][hapmap]
rs3185	0.89[JPT][hapmap]
rs3923920	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4072131	0.81[YRI][hapmap]
rs4073790	0.88[ASN][1000 genomes]
rs4073791	0.88[ASN][1000 genomes]
rs4244451	0.81[ASN][1000 genomes]
rs4244452	0.83[ASN][1000 genomes]
rs4244453	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4244454	0.81[CEU][hapmap]
rs4273861	0.87[ASN][1000 genomes]
rs4292704	0.89[JPT][hapmap]
rs4311666	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4317590	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4319111	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4339658	0.88[ASN][1000 genomes]
rs4410924	0.87[CEU][hapmap]
rs4413788	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4442163	0.92[ASN][1000 genomes]
rs4455848	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4472532	0.86[CHD][hapmap]
rs4483172	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4484715	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4513991	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4524812	0.83[ASN][1000 genomes]
rs4554481	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4599829	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4614013	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4631482	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4631483	0.86[ASN][1000 genomes]
rs4921646	0.83[ASN][1000 genomes]
rs4921647	0.82[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4921648	0.89[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs4921649	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs4921651	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4921652	0.93[ASN][1000 genomes]
rs4921653	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4921654	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4921655	0.86[ASN][1000 genomes]
rs4921656	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4921657	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4922030	0.81[YRI][hapmap]
rs4922034	0.81[ASN][1000 genomes]
rs4922036	0.89[JPT][hapmap]
rs4922037	0.89[ASN][1000 genomes]
rs4922038	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4922039	0.95[ASN][1000 genomes]
rs4922041	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4922044	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4922045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4922046	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4922047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4922048	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4922049	0.92[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4922065	0.87[CEU][hapmap]
rs5013219	0.83[ASN][1000 genomes]
rs6586836	0.81[ASN][1000 genomes]
rs6586837	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6586838	0.81[ASN][1000 genomes]
rs6586839	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6586840	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6586842	0.87[TSI][hapmap]
rs6586843	0.87[CEU][hapmap]
rs6984449	0.89[JPT][hapmap]
rs6984644	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6988743	0.90[ASN][1000 genomes]
rs6991941	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6994352	0.82[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6998991	0.95[ASN][1000 genomes]
rs6999542	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7002643	0.82[CHD][hapmap]
rs7005075	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7017776	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73585587	0.82[ASN][1000 genomes]
rs7460541	0.92[ASN][1000 genomes]
rs7464357	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7464358	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7814548	0.87[CHD][hapmap]
rs7816777	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7818691	1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs7828197	0.85[ASN][1000 genomes]
rs7830404	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7838412	0.87[CEU][hapmap]
rs7839041	0.82[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7841402	0.81[CEU][hapmap]
rs9644628	0.90[ASN][1000 genomes]
rs9644629	0.90[ASN][1000 genomes]
rs9644630	0.88[ASN][1000 genomes]
rs9644631	0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	esv3693374	chr8:19241970-19359184	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv890623	chr8:19307051-19383697	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv890624	chr8:19319061-19456270	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6998334	PDGFRL	cis	cerebellum	SCAN
rs6998334	CSGALNACT1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19310600-19359600	Weak transcription	Ovary	ovary
2	chr8:19319600-19362800	Weak transcription	Spleen	Spleen
3	chr8:19331000-19352800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr8:19333400-19362200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr8:19338000-19351000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr8:19338800-19370600	Weak transcription	Esophagus	oesophagus
7	chr8:19339000-19351800	Weak transcription	Primary B cells from cord blood	blood
8	chr8:19339400-19352800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr8:19340000-19348400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr8:19340000-19352800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr8:19341200-19351000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr8:19341400-19354200	Weak transcription	Brain Substantia Nigra	brain
13	chr8:19341800-19351600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr8:19343800-19348600	Enhancers	Fetal Brain Male	brain
15	chr8:19344000-19349600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr8:19344000-19351800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr8:19344400-19351600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr8:19345000-19349600	Weak transcription	Gastric	stomach
19	chr8:19345200-19353000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr8:19345400-19349200	Weak transcription	Stomach Mucosa	stomach
21	chr8:19346200-19348200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:19346200-19348200	Enhancers	A549	lung
23	chr8:19346400-19348400	Enhancers	Brain Cingulate Gyrus	brain
24	chr8:19346400-19357000	Weak transcription	Fetal Lung	lung
25	chr8:19347000-19348200	Enhancers	Brain Angular Gyrus	brain
26	chr8:19347200-19348200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr8:19347200-19348200	Enhancers	Fetal Brain Female	brain
28	chr8:19347200-19350200	Weak transcription	Primary T cells from cord blood	blood
29	chr8:19347400-19348400	Enhancers	Right Atrium	heart
30	chr8:19347400-19348400	Enhancers	Right Ventricle	heart
31	chr8:19347600-19348200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr8:19347600-19348200	Enhancers	Brain Anterior Caudate	brain
33	chr8:19347600-19348400	Enhancers	Left Ventricle	heart
34	chr8:19347600-19348600	Strong transcription	Placenta	Placenta
35	chr8:19347800-19348200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr8:19347800-19348200	Enhancers	Brain Hippocampus Middle	brain
37	chr8:19347800-19348600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr8:19347800-19351600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr8:19348000-19348200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr8:19348000-19348200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:19348000-19348200	Enhancers	Lung	lung
42	chr8:19348000-19348400	Enhancers	H9 Cell Line	embryonic stem cell
43	chr8:19348000-19376600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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